CCP4 Study Weekend 2014 What’s new in CCP4 Ronan Keegan, CCP4, Research Complex at Harwell

1. CCP4 Study Weekend 2014What’s new in CCP4Ronan Keegan, CCP4, Research Complex at Harwell

2. Overview • “What’s new in CCP4” • Ronan Keegan (CCP4, Research Complex at Harwell) • “Refmac and ProSMART” • Rob Nicholls (LMB-MRC Cambridge) • “AMPLE – ab initio modelling for molecular replacement” • Jens Thomas (University of Liverpool) • “DIALS – diffraction integration for advanced light sources” • David Waterman (CCP4, Research Complex at Harwell) • “Multiple crystals data combination with BLEND” • James Foadi (Diamond Light Source)

3. Outline • What is CCP4? • Brief tour of CCP4 current release • Major developments that should appear within the next 12-18 months

4. Lunchtime Bytes • Coot - B. Lohkamp • CCP4mg - S. McNicholas • CCP4i2 (GUI2) – L. Potterton • MrBUMP / AMPLE - J. Thomas/D. Rigden/R. Keegan • Aimless / Pointless - P. Evans • Mosflm / iMosflm - H. Powell • Phaser - A. McCoy/R. Read • Buccaneer / Nautilus - K. Cowtan (4th Jan. only) • Crank - P. Skubak/R. Pannu (5th Jan. only) • PiMS - C. Morris (4th Jan. only) • Balbes - F. Long • Refmac / ProSMART - R. Nicholls • CCPEM – C. Wood/T. Burnley • CCPBioSim – H. Loeffler (5th Jan. only) Bytes

5. What is CCP4? • CCP4 stands for “Collaborative Computational Project Number 4” • One of several CCPs set up in the UK to advance and support scientific software development • CCP4 was set up in the late 1970’s to bring together the leading developers of software in the field of protein X-ray crystallography in the UK • The aim was to assemble a comprehensive collection of software to satisfy the computational requirements of the relevant UK groups

6. Core Group (Oxford): • Maintain and support software suite • Application and infrastructural software developments • Collaborate with Diamond on software deployment on the beamline • Educational outreach • Maintaining CCP4 resources such as the CCP4 bulletin board • Cambridge: • Laboratory of Medical Biology • Data processing software - Mosflm, Aimless • Refinement software – Refmac • Model building - Coot • University of Cambridge • Phaser group • University of York: • Software development – CCP4mg, Buccaneer, Nautilus • CCP4 GUI2 development • Others include the Crank group at Leiden in the Netherlands and AMPLE developers at the University of Liverpool York Cambridge CCP4

7. CCP4 Usage

8. CCP4 Schools/Workshops • Main aim is to give education and expert help to researchers working with collected crystal data • Some schools also provide expert help with collecting crystal data (APS & Hamburg) • Applicants with challenging crystals and/or data are given strong consideration but this is not mandatory • Software developers from CCP4, Phenix (APS), Shelx, ARP/wARP, XDS and HKL as well as others give lectures, tutorials and are also available to help with data processing and structure solution throughout the meetings • http://www.ccp4.ac.uk– Courses & Events

9. 2014 CCP4 Schools/Workshops • Brazil: Sao Carlos, April 8th – 16th 2014 • APS/CCP4 Summer School: APS Synchrotron, Chicago, USA June 24 – July 2 2014 • http://www.ccp4.ac.uk/schools/APS-2014 • BCA Summer School: Oxford, September 2014 • DLS/CCP4 workshop: Diamond Synchrotron, Oxford, December 2014. • Japan 2014

10. Other Resources • CCP4BB mailing list – bulletin board, news, expert help and advice • CCP4 help desk – ccp4@ccp4.ac.uk – bug reports, problems with software • CCP4 wiki – http://ccp4wiki.org– program documentation and tutorials • CCP4 web page – http://www.ccp4.ac.uk

11. The CCP4 software suite • The CCP4 suite is a comprehensive suite of software for protein crystallography • New versions of the suite are released about every 12 months • New programs • Major updates to existing programs • Other new features such as changes to CCP4i interface • New - Revisions to the current release are made available through the CCP4 updates manager

12. CCP4 Software Molecular Replacement Experimental Phasing Model Building Refinement Density Modification Data Processing and Reduction Structure Analysis Data Collection Crystallisation Deposition

13. CCP4 Releases • Current Release Version - CCP4 6.4 • Several new programs in 6.3/4: • QTPisa, Aimless, Dimple, AMPLE, Zanuda, ProSMART, Nautilus, Ensembler, Sculptor, Jligand, • Coot – integrated with suite • In collaboration with the EMBL Hamburg, ARP/wARP is now rolled with the CCP4 suite • Continuing development of major components • Phaser, Refmac, Mosflm/iMosflm, Crank, MrBUMP • New infrastructure • Build system, Downloads manager and Updates Manager

14. Data Processing and Reduction Bytes iMosflm Coming soon: Multiple lattice processing Parallelisation – quickens processing See Harry during lunchtime bytes session for more details

15. Data Processing and Reduction Bytes Pointless Determine point-group (& space group) Aimless Scale-symmetry-related intensities together Produce statistics on data quality Replacement for Scala See Phil during lunch-time bytes for more details

16. Data Processing and Reduction • Automated data-reduction – from diffraction images to merged reflection file Dimple • On-beamline rapid calculation of difference maps to ascertain success or failure of ligand binding

17. Experimental Phasing Crank Bytes • Automated experimental phasing pipeline • Heavy atom location through to Model Building Bytes Phaser EP • Automated experimental phasing • SAD phasing • Combined MR and SAD Phasing

18. Molecular Replacement Bytes Phaser MR • Automated Maximum Likelihood method for molecular replacement • Twinning • Translational NCS • σrms refinement Molrep • Molecular Replacement • Phased Rotation/Translation function • Multi-copy search • New interface in 6.4.0

19. Molecular Replacement – Search model preparation Sculptor • Multi-protocol search model preparation • weighted sequence similarity • accessible surface area Ensembler • Ensemble search model generation tool from the developers of Phaser Molrep & Chainsaw • Search model preparation using internal sequence alignment or provided alignment

20. Molecular Replacement - Automation MrBUMP • Automated molecular replacement • From model search and preparation through to initial refinement • Uses Phaser and Molrep • Now includes Model building options Bytes BALBES • Automated molecular replacement using Molrep and Refmac • Custom DB with search models monomer, domain and multimeric form Bytes

21. BALBES Webservice http://www.ccp4.ac.uk/BALBESSERV or Google for“BALBES”

22. Molecular Replacement – Ab initio search models AMPLE • Generate and prepare ab initio or de novo models using Rosetta and other software for use as search models in molecular replacement • Works well for smaller, α-helical proteins (<120 residues) but has been known to work for larger targets • Requires installation of several third-party applications such as Rosetta Bytes

23. Density Improvement Parrot • Uses maximum likelihood methods and builds on original DM program • Fast and fully automated Bytes Pirate • Statistical-based density modification • Better in some cases but slower than Parrot

24. Model Building Buccaneer • Chain tracing by identifying connected alpha-carbon positions using a likelihood-based density target • Low resolution model building See Kevin during lunch-time bytes for more details Bytes Nautilus • Automatic model building of nucleotide structures in electron density maps Sloop • Loop building by finding gaps in the chain and using fragments from the Richardson's Top500 library of structures to fill the gaps

25. Model Building ARP/wARP 7.4 • Automated building of • proteins • RNA/DNA • secondary structure • side chains • loops • solvent • ligands • Now jointly distributed by CCP4

26. Model Building - Coot • Coot 0.7.2 • RCrane and Cootaneer for RNA building • Ligand Builder working in conjunction with ProDRG • Jligandinterface • External restraints • Morphing Bytes

27. Model Building: ligand building Jligand • Generate and regularise ligands • Link ligands together and generate link description

28. Refinement Refmac 5.8 • Improved jelly body refinement • Improved use of restraint information (ProSMART) • DNA/RNA base pair restraints • Suger/pucker restraints • Simultaneous density modification and refinement (initially SAD, more general later) • Better anomalous difference maps • Beta ensemble refinement • Multi-imputation and averaging of structure factors to desired resolution • Sampling of conformational space – Gibbs sampling • Estimation of individual errors of atoms – less biased electron density calculation Bytes

29. Refinement ProSMART Bytes • Structure alignment • Generation of external restraints for use in refinement ProDrg • Generate restraints for ligands for use in refinement and model building Zanuda • Analyse refinement results • Check correct space group

30. Structure Analysis QtPISA • Automatic inference on multimeric states from crystal packing • Analysis of macromolecular interfaces and macromolecular interactions • QTPisa – new QT based interface

31. Structure Analysis CCP4MG 2.8.0 Bytes Gesamt • Replacement for Superpose • Improved secondary structure alignment

32. Report Viewer - QTRview • Graphical log file viewer • View graphs, tables and job summary information • Launch Coot, CCP4mg and ViewHKL to view data files • Can still view original log file

33. Update Manager • Automatically install latest fixes and new features • Allows for rolling back to previous versions • Updates made available once every two weeks or as and when they are needed • Available on Linux, Mac and Windows • Recent updates: • ARP/wARP • Aimless • MrBUMP • Ctruncate

34. Downloading the suite • Download CCP4 for Windows, Mac or Linux • Co-distribution of ARP/wARP • Package Manager – easy installation • 64-bit Mac version • Additional software dependencies also available • Download page accessible from • http://www.ccp4.ac.uk

35. Package Manager • Easy installation mechanism for CCP4 and associated packages (Coot, ARP/wARP, CCP4mg) • Available on Linux, Mac and Windows • Sets up system variables automatically if you wish

36. Developments • DIALS – data processing software • CRANK2 – experimental phasing • GUI2 – replacement for CCP4 • Refmac, monomer library, AMPLE covered in dedicated talks by Rob Nicholls and Jens Thomas

37. Developments - DIALS • Diffraction Integration for Advanced Light Sources • New data processing software designed for: speed, flexibility and accuracy, esp. with challenging data • Will cater for both synchrotron and XFEL experiments • Main philosophy: build a comprehensive toolkit. Thus implementing both 3D and 1D FFT indexing methods, 2D and 3D integration methods, multiple optimisation engines and allowing extension through an algorithm plug-in system http://dials.sourceforge.net/

38. Developments – CRANK2 (Leiden) Bytes Combined SAD workflow Pannu & Skubak, Nature Comm Aug. 2013 Step wise workflow

39. Developments – CRANK2 • Example: 12 subunit RNA polymerase II • 3.8A resolution dataset with anomalous signal from eight intrinsic zinc ions (Meyer P.A. et al., J.Biol.Chem., 2009) • ~4000 residues in the asym. unit; no NCS • Originally solved by a partial model MR followed by multi-crystal MAD phasing, MR-MAD phase combination and manual iterative model building • The new combined approach in CRANK can build ~70% of the protein backbone automatically from a single SAD dataset only, with R-free of 37.5%

40. Developments – CRANK2 • Currently available directly from Leiden group • Will be released as an update to CCP4 6.4 See Raj and Pavol during lunch-time bytes for more details

41. Developments – GUI2 Bytes • Written in PyQt • Build on 10 yrs of CCP4i • Designed to be simple • Simple input/output • Hints • Also expert view • Database used for data tracking See Liz during lunchtime bytes session for more details

42. Acknowledgements • CCP4 Core group: Andrey Lebedev, Eugene Krissinel, Charles Ballard, David Waterman, Marcin Wojdyr, Ville Uski, Karen McIntyre, Carol Malpass, Martyn Winn • LMB/MRC: Andrew Leslie, Phil Evans, Garib Murshudov, Rob Nicholls, Harry Powell, Owen Johnson, Fei Long, Paul Emsley, Andrea Thorn • Phaser Group: Airlie McCoy, Randy Read, Rob Oeffner, Gabor Bunkoczi • YSBL York: Keith Wilson, Kevin Cowtan, Liz Potterton, Stuart McNicholas, Eleanor Dodson • Diamond: GwyndafEvans, Graeme Winter • Leiden: Raj Pannu, Pavol Skubak • Others: Bernhard Lohkamp, Clemens Vonrhein, Ruslan Sanishvili, Frank Von Delft, Martin Noble, Jaclyn Bibby, Daniel Rigden, Jens Thomas, Alun Ashton, David Brown, Arwen Pearson, Tim Gruene, George Sheldrick and many more..

43. Lunchtime Bytes • Coot - B. Lohkamp • CCP4mg - S. McNicholas • CCP4i2(GUI2) – L. Potterton • MrBUMP / AMPLE - J. Thomas/D. Rigden/R. Keegan • Aimless / Pointless - P. Evans • Mosflm / iMosflm - H. Powell • Phaser - A. McCoy/R. Read • Buccaneer / Nautilus - K. Cowtan (4th Jan. only) • Crank - P. Skubak/R. Pannu (5th Jan. only) • PiMS - C. Morris (4th Jan. only) • Balbes - F. Long • Refmac / ProSMART - R. Nicholls • CCPEM – C. Wood/T. Burnley • CCPBioSim – H. Loeffler (5th Jan. only) Bytes